Mercurial > repos > galaxyp > hirieftools

annotate align_dbspec.py @ 2:77ddaee887a8 draft

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planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
author galaxyp
date Fri, 01 Sep 2017 03:14:54 -0400
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2
77ddaee887a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
galaxyp
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diff changeset
1 #!/usr/bin/env python
77ddaee887a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
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2 import sys
77ddaee887a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
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3 import os
77ddaee887a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
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4 import argparse
77ddaee887a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
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5 import re
77ddaee887a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
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6 from Bio import SeqIO
77ddaee887a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
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7
77ddaee887a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
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8
77ddaee887a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
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9 def create_spectra_maps(specfiles, dbfiles, frregex, firstfr):
77ddaee887a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
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10 """Output something like
77ddaee887a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
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11 {'fr01', 'fr04'} # Normal filename set
77ddaee887a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
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12 and
77ddaee887a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
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13 {'fr03': ['fr02', 'fr03']} # pool definition
77ddaee887a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
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14 and
77ddaee887a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
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15 {'fr04': 'fr04', 'fr04b': 'fr04'} # rerun fraction, rerun may also be pool
77ddaee887a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
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16 """
77ddaee887a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
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17 specrange = get_fn_fractionmap(specfiles, frregex)
77ddaee887a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
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18 to_pool = []
77ddaee887a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
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19 poolmap, rerun_map, normal_fns = {}, [], set()
77ddaee887a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
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20 for i in range(0, len(dbfiles)):
77ddaee887a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
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21 num = i + firstfr
77ddaee887a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
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22 if num not in specrange:
77ddaee887a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
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23 to_pool.append(i)
77ddaee887a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
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24 elif to_pool and num in specrange:
77ddaee887a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
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25 to_pool.append(i)
77ddaee887a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
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26 poolmap[specrange[num][0]] = to_pool
77ddaee887a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
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27 to_pool = []
77ddaee887a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
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28 if not to_pool and specrange[num][0] in poolmap:
77ddaee887a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
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29 if poolmap[specrange[num][0]][-1] != i:
77ddaee887a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
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30 normal_fns.add((dbfiles[num - 1],
77ddaee887a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
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31 specfiles[specrange[num][0]]))
77ddaee887a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
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32 elif not to_pool:
77ddaee887a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
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33 normal_fns.add((dbfiles[num - 1], specfiles[specrange[num][0]]))
77ddaee887a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
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34 for num in sorted(specrange.keys()):
77ddaee887a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
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35 if len(specrange[num]) > 1:
77ddaee887a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
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36 rerun_map.append(specrange[num])
77ddaee887a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
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37 return normal_fns, rerun_map, poolmap
77ddaee887a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
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38
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39
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40 def get_fn_fractionmap(files, frregex):
77ddaee887a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
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41 fnfrmap = {}
77ddaee887a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
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42 for f_ix, fn in enumerate(files):
77ddaee887a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
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43 fnum = int(re.sub(frregex, '\\1', fn))
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44 try:
77ddaee887a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
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45 fnfrmap[fnum].append(f_ix)
77ddaee887a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
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46 except KeyError:
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47 fnfrmap[fnum] = [f_ix]
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48 return fnfrmap
77ddaee887a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
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49
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50
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51 def pool_fasta_files(poolfiles):
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52 acc_seq = {}
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53 for fr in poolfiles:
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54 for seq in SeqIO.parse(fr, 'fasta'):
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55 sequence = str(seq.seq.upper())
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56 try:
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57 if sequence in acc_seq[seq.id]:
77ddaee887a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
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58 continue
77ddaee887a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
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59 except KeyError:
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60 acc_seq[seq.id] = {sequence: 1}
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61 yield seq
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62 else:
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63 acc_seq[seq.id][sequence] = 1
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64 yield seq
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65
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66
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67 def write_pooled_fasta(poolmap, specnames, dbfiles):
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68 """Runs through poolmap and pooles output files, filtering out
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69 duplicates"""
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70 for outfr, infrs in poolmap.items():
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71 outfn = os.path.join('aligned_out', os.path.basename(specnames[outfr]))
77ddaee887a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
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72 print('Pooling FASTA files {} - {} into: {}'.format(
77ddaee887a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
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73 dbfiles[infrs[0]], dbfiles[infrs[-1]], outfn))
77ddaee887a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
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74 with open(outfn, 'w') as fp:
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75 SeqIO.write(pool_fasta_files([dbfiles[x] for x in infrs]), fp,
77ddaee887a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
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76 'fasta')
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77
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78
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79 def write_nonpooled_fasta(fractions):
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80 """Symlinks nonpooled db files"""
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81 print('Symlinking non-pooled non-rerun files',
77ddaee887a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
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82 [(fr[0], os.path.join('aligned_out', os.path.basename(fr[1])))
77ddaee887a8 planemo upload for repository https://github.com/galaxyproteomics/tools-galaxyp/tools/pi_db_tools commit 71a4265d11aef48342142b8cf2caa86f79f9a554
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83 for fr in fractions])
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84 [os.symlink(fr[0], os.path.join('aligned_out', os.path.basename(fr[1])))
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85 for fr in fractions]
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86
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87
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88 def copy_rerun_fasta(rerun_map, specnames):
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89 for dst_indices in rerun_map:
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90 src = os.path.join(specnames[dst_indices[0]])
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91 for outfn in [specnames[x] for x in dst_indices[1:]]:
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92 print('Symlinking {} to {}'.format(src, outfn))
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93 os.symlink(src, os.path.join('aligned_out', outfn))
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94
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95
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96 def main():
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97 args = parse_commandline()
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98 with open(args.spectranames) as fp:
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99 spectranames = [x.strip() for x in fp.read().strip().split('\n')]
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100 vanilla_fr, rerun_map, poolmap = create_spectra_maps(spectranames,
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101 args.dbfiles,
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102 args.frspecregex,
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103 args.firstfr)
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104 write_pooled_fasta(poolmap, spectranames, args.dbfiles)
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105 write_nonpooled_fasta(vanilla_fr)
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106 copy_rerun_fasta(rerun_map, spectranames)
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107
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108
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109 def parse_commandline():
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110 parser = argparse.ArgumentParser(
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111 formatter_class=argparse.RawTextHelpFormatter)
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112 parser.add_argument('--specnames', dest='spectranames', help='File '
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113 'containing spectra filenames with fractions. '
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114 'Test data example illustrates reruns (fr03b, 09b) and'
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115 ' pooled samples (fr05-09 are inside fr09 and fr09b).',
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116 required=True)
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117 parser.add_argument('--dbfiles', dest='dbfiles', help='FASTA db files',
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118 nargs='+', required=True)
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119 parser.add_argument('--frspec', dest='frspecregex', help='Fraction regex '
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120 'to detect spectra fraction numbers', required=True)
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121 parser.add_argument('--firstfr', dest='firstfr', help='First fraction nr',
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122 type=int, required=True)
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123 return parser.parse_args(sys.argv[1:])
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124
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125
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126 if __name__ == '__main__':
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127 main()